Make sure that docker entrypoint works for integration tests

pvannierop · Aug 22, 2023 · 6c230db · 6c230db
1 parent f91d0fd
commit 6c230db
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml
@@ -42,8 +42,12 @@ jobs:
         working-directory: ./cbioportal-docker-compose
         run: |
           cd ./data && ./init.sh && rm -rf ./studies/* && cd ../config && \
-          cat $PORTAL_SOURCE_DIR/portal/target/portal/WEB-INF/classes/portal.properties | \
-              sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|g' \
+          cat $PORTAL_SOURCE_DIR/portal/target/classes/portal.properties | \
+              # TODO: remove 4 lines below after upgrade of cbioportal-docker-compose to > v5.3.20
+              sed 's|db.host=.*||' | \
+              sed 's|db.portal_db_name=.*||' | \
+              sed 's|db.use_ssl=.*||' | \
+              sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false&allowPublicKeyRetrieval=true|' \
               > portal.properties
       - name: 'Start cbioportal-docker-compose'
         working-directory: ./cbioportal-docker-compose

diff --git a/docker/web-and-data/docker-entrypoint.sh b/docker/web-and-data/docker-entrypoint.sh
@@ -109,12 +109,16 @@ migrate_db() {
 _main() {
     # when running the webapp, check db and do migration first
     # check if command is something like "java -jar webapp-runner.jar"
+    if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then
+        echo Running: "$@"
+    fi
+
     if [[ "$@" == *java* ]] && [[ "$@" == *-jar* ]] && [[ "$@" == *webapp-runner.jar* ]]; then
         # Parse database config. Use command line parameters (e.g. -Ddb.host) if
         # available, otherwise use portal.properties
         if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then
             echo "Using database config:"
-            #parse_db_params_from_config_and_command_line $@
+            parse_db_params_from_config_and_command_line $@
         fi
 
         check_db_connection $@

diff --git a/test/integration/docker-compose-localbuild.yml b/test/integration/docker-compose-localbuild.yml
@@ -6,10 +6,13 @@ version: '3'
 services:
   cbioportal:
     command: /bin/sh -c "java -Xms2g -Xmx4g -Dauthenticate=noauthsessionservice -Dsession.service.url=http://cbioportal_session:5000/api/sessions/my_portal/ -jar webapp-runner.jar -AmaxHttpHeaderSize=16384 -AconnectionTimeout=20000 --enable-compression /app.war"
+#    command: tail -f /dev/null
     volumes:
      - $PORTAL_INFO_DIR:/portalinfo/
      # make docker compose run the cbioportal version-under-test
      # by volume mounting the local portal source folder into the container
      # and running
      - $PORTAL_SOURCE_DIR:/cbioportal/
      - $PORTAL_SOURCE_DIR/portal/target/cbioportal.war:/app.war
+     # TODO: remove line below after upgrade of cbioportal-docker-compose to > v5.3.20
+     - $PORTAL_SOURCE_DIR/docker/web-and-data/docker-entrypoint.sh:/usr/local/bin/docker-entrypoint.sh